Molecular basis of foreign DNA recognition by BREX anti-phage immunity system
Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.
Authors
- Mikhail E. Matlashov (ORCID: https://orcid.org/0000-0003-0769-4749)
- Tim R. Blower (ORCID: https://orcid.org/0000-0002-7390-6458)
- Myfanwy C. Adams (ORCID: https://orcid.org/0000-0001-5918-0411)
- Karen L. Maxwell (ORCID: https://orcid.org/0000-0002-0211-5480)
- Konstantin Severinov (ORCID: https://orcid.org/0000-0001-9706-450X)
- Anna Trofimova (ORCID: https://orcid.org/0009-0005-3111-8559)
- Artem Isaev (ORCID: https://orcid.org/0000-0002-9593-2745)
- Mikhail Skutel (ORCID: https://orcid.org/0009-0002-1351-3238)
- Alena Drobiazko (ORCID: https://orcid.org/0000-0001-9290-2498)
- Dmitry Ghilarov (ORCID: https://orcid.org/0000-0001-9325-3207)
- Kristina Potekhina
- Oksana Kotovskaya
- Daria Yatselenko
Institutions
- John Innes Centre (GB)
- Rutgers, The State University of New Jersey (US)
- Skolkovo Institute of Science and Technology (RU)
- University of Toronto (CA)
- Durham University (GB)
- Institute of Gene Biology (RU)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-02-20
- DOI
- https://doi.org/10.1038/s41467-025-57006-2
- Citations
- 14
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 24.03
Funders
- Wellcome Trust
- Lister Institute of Preventive Medicine
- Russian Science Foundation
- Skolkovo Institute of Science and Technology
- Canadian Institutes of Health Research
- Biotechnology and Biological Sciences Research Council